Award-Winners Mentor Award-Winners

Mentoring deepens education across the University and academic fields, although it has become particularly noticeable in science laboratories during CUNY's Decade of Science. The record 16 students and alumni who won National Science Foundation Graduate Research Fellowships in 2012 could point to a CUNY mentor who helped set them on a path of scientific inquiry. No public university in the Northeast had more NSF winners than CUNY, a testament to the resurgence of a University that attracts an ever-growing number of top-tier students and prepares them for an ever-more-prestigious list of graduate schools, fellowships and opportunities.


Astronomy and Astrophysics

Dr. Kelle Cruz

Assistant Professor
Physics and Astronomy, Hunter College
National Science Foundation Partnerships in Astronomy and Astrophysics 2012-2017

Vivienne Baldassare

Macaulay Honors College at Hunter College
National Science Foundation
Graduate Research Fellow 2012

There are few things that make teachers prouder than when a student nails it. Just ask Kelle Cruz, an assistant professor of astronomy and astrophysics at Hunter College, about an undergraduate she mentored last year, Vivienne Baldassare.

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Cruz asked Baldassare (Macaulay Honors College at Hunter College, B.A. in physics, 2012) to help with research into brown dwarfs. These are wannabe stars – bigger than gas giant planets, smaller than stars and lacking an energy source at their core.

“Vivienne had never reduced data before,” Cruz recalls, meaning she had never cleaned up raw data from a telescope to remove artifacts from electronics, Earth’s atmosphere and other sources of contamination. “It’s an astronomical version of Photoshop that makes data closer to reality,” Cruz says.

In research into the age and evolution of brown dwarfs, Baldassare measured information on how fast some of them were moving away from or toward Earth, which is shown by red-shifted or blue-shifted spectra, respectively. “Vivienne wrote code to measure the wavelength shift in kilometers per second, handed me the final table, with all the results, with a bow on it and said, ‘See you at the next AAS [American Astronomical Society] meeting.’ It was wonderful,” Cruz says.

And then Baldassare took off for a doctoral program at the University of Michigan-Ann Arbor where, with an NSF graduate research fellowship, she intends to look at collisions of ultra-luminous infrared galaxies – that is, galaxies that emit 1012 times more infrared light that our sun.

“I hope that my research will contribute to our understanding of the role that galaxy mergers and active galactic nuclei play in galaxy evolution,” she says.

Cruz and Baldassare met at the American Museum of Natural History, where all CUNY astronomers hold appointments and CUNY students are welcome to be part of the community. At the time, Baldassare was wrapping up study with associate professor Charles Liu of the College of Staten Island; the time was right to move onto a new mentor and a new area of study. Liu had changed her life by asking her to classify galaxies according to their shapes.

“I'd never thought about astronomy as a career, but I found I loved it,” she says.

Cruz typically mentors about seven students in her lab, from undergraduate to post-doctoral. This year, she even recruited a high school graduate who just enrolled at Macaulay Honors College. Her protégés are a diverse group that includes not only astronomers but also programmers, since so much of astrophysics these days is done with computers.

“We work together as a team, and I meet with them one-on-one at least weekly to help them reach whatever goal they’re trying to achieve,” Cruz says. “If I have an opinion about what they’re doing, I give it, whether it’s ‘Why do you live so far away?’ or ‘Have you thought about that class schedule?’ to real scientific issues. I think of myself more as a career coach. We don’t talk about ‘How can you program better?’ but ‘How can you network better? How can you balance your work life better?’ All aspects of a career are on the table.”

Cruz is investigating what she calls “weird or peculiar” young brown dwarfs, with young being 50 million years old, versus the more common gigayear- (billion-year-) old brown dwarf. She’s looking at youngsters that are solitary, rather than huddling in clusters, as really young stars tend to do.

“The bigger picture is in star formation – how stars grow up” and how large gaseous planets like Jupiter come into being, she says. “The young brown dwarfs are brighter, so we can study them more easily than exoplanets [planets outside our solar system], which show up as tiny specks next to bright stars. By figuring out the evolution of brown dwarfs, we also hope to better understand giant exoplanets like Jupiter.”

Her research has been supported by a National Science Foundation Partnerships in Astronomy & Astrophysics in Research and Education grant; the NASA Astronomy and Data Analysis Program; and the NASA Hubble Space Telescope, Cycle 19 (The Formation and Fundamental Properties of Wide Planetary-Mass Companions).

Cruz-Baldassare



Molecular Regulation of Oogenesis

Dr. Gerard McNeil

Associate Professor
Biology, York College
National Institutes of Health MBRS/SCORE 2010-2014

Kirk Haltaufderhyde

York College
National Science Foundation
Graduate Research Fellow 2012

York College associate professor Gerard McNeil has found a way to expand mentoring beyond the limits of his small biology research laboratory to the broader world of his classroom.

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Traditional classroom lab experiments differ starkly from those conducted in research labs; while classroom experiments demonstrate results that are already known, research seeks to discover new information. The research lab is thus the more exciting place for students who may become scientists, but there’s a bottleneck.

“There are so few research labs and so many students, but you can give many more students a research experience by bringing real-life scientific problems into the classroom,” he says.

So McNeil teamed up with the Genomics Education Partnership, a consortium based at Washington University in St. Louis. Funded by the Howard Hughes Medical Institute, the partnership allows students at more than 80 undergraduate colleges nationwide to engage in bioinformatics (using computers to study vast amounts of biological data, like genomes).

“We use computers as tools for students to answer unknown biological questions in the classroom,” he says. “The students at each institution get their own piece of the genomics puzzle. They learn to gather data, use the required tools and develop and test hypotheses. Those skills are applicable to every area of science. All the data is captured at Washington University, which puts it together and makes sense of it at the genomic level. Before, we needed a wet lab and a lot of room to ask unknown biological questions; now all you need is a computer.”

Which is not to say that McNeil doesn’t engage in one-on-one mentoring and old-fashioned wet bench work in his lab. Since 2002, his research and mentoring have been supported by the National Institutes of Health-Minority Biomedical Research Support/Support of Competitive Research (SCORE) program. SCORE seeks to increase the research capabilities and competitiveness of investigators at colleges like York, where at least half the students are from groups that are underrepresented in biomedical and behavioral research.

McNeil’s lab focuses on the genetics behind oogenesis, the formation, development and maturation of ova, or egg cells. He’s particularly interested in the impact of a maternally acting gene called lark, which encodes an RNA-binding protein that is essential for oogenesis. Although he uses the fruit fly Drosophila melanogaster as a model system to study this gene, a human version has been identified and studied.

“Evolution has found a way to use this protein for multiple purposes rather than creating new genes,” McNeil explains. “There are lots of cases like this. Sometimes it does the same things in different tissues; sometimes it does different things. This gene probably plays a role in RNA metabolism in the nucleus during many developmental stages and in translation in the cytoplasm in others. However, we’re still learning new things every day.”

With McNeil as his mentor, 2012 NSF winner Kirk Haltaufderhyde (York College, B.S. in biotechnology, 2011) chose a career in science after having interrupted his studies to support his family, working in the audio-video industry for some years. Tapping into data provided by the Genomics Education Partnership, he completed three original research projects on the genomes of two less-studied species of Drosophila, comparing them to the well-known fruit fly that is McNeil’s model. He also is a co-author on a manuscript that is in preparation.

“Working from an already well characterized D. melanogaster genome, we can use computer software to perform a comparative analysis of DNA sequences from other Drosophila species to detect genes of common ancestry,” Haltaufderhyde says. “These are called orthologous genes.”

Those projects, he says, looked at the gene-rich region of the fourth chromosome of several Drosophila species, seeking insight into gene structure, repeat types, densities and evolution in different species of this form of chromatin (the complex of DNA and proteins in the cell nucleus that is essential for maintaining chromosome structure).

Haltaufderhyde, 32, says that he “went to York because I was able to get close interaction with all the professors, and you might not get that at other institutions. To have the research experience with Doctor McNeil was definitely a turning point.”

McNeil says that “when you find a student like Kirk, you grab him.” They met when he was taking McNeil’s General Biology 2 class and asked for a letter of recommendation for a summer research program. “I said, ‘What about my lab?’ He had not thought about graduate school, so we spent the summer talking about that as he did research.”

Haltaufderhyde is pursuing a doctorate at Brown University.

McNeil-Haltaufderhyde



Learning and Memory

Dr. Jennifer Mangels

Professor Psychology, Baruch College
National Science
Foundation Award 2009-2012

Belén Carolina Guerra-Carillo

Baruch College
National Science Foundation
Graduate Research Fellow 2012

The right mentor can change a student’s life – and possibly trigger a cascade of mentoring that ripples through the next generation of students. At least, that’s the experience of cognitive neuropsychologist Jennifer Mangels, a professor at Baruch College and The City University of New York Graduate Center.

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Her research into how people learn – particularly from mistakes – has won support from the federal Institute of Educational Sciences, National Institutes of Health, National Science Foundation and Army Research Laboratory, among others. In 2012, two undergraduate students in her Dynamic Learning Lab won $126,000 National Science Foundation (NSF) Graduate Research Fellowships; she mentored one closely and helped the other perfect her NSF application.

“I’m only here as a professor because I had a great mentor as an undergraduate,” Mangels says. At the University of Delaware, professor Helen Intraub “saw my potential and put as much into me as she would have put into a graduate student. She believed in me and said, ‘You have an interest. Here’s a project. Figure it out.’ That’s what I do for my students. I treat them like the integral part of the research team that they are. I always have the undergraduates up at the front for lab meetings, so they feel they’re as much a part of the process as my graduate students. If they are close, I can better read their faces to see if they are with me or not and adjust the level of detail in my presentation. When they understand more fully, they can participate in the research process more fully.”

Mentoring deepens education across the University and academic fields, although it has become particularly noticeable in science laboratories during CUNY’s Decade of Science. The record 16 students and alumni who won NSF awards in 2012 could point to a CUNY mentor who helped set them on a path of scientific inquiry. No public university in the Northeast had more NSF winners than CUNY, a testament to the resurgence of a University that attracts an ever-growing number of top-tier students and prepares them for an ever-more-prestigious list of graduate schools, fellowships and opportunities.

Consider NSF winner Belén Carolina Guerra-Carrillo (Baruch, B.A. in psychology, 2010), who was so intrigued with her research that she signed on to manage Mangels’ lab for two years after graduation. “I was able to research full time and to help in many projects, seeing them through from beginning to end,” she says. “Doctor Mangels is a great mentor.”

This fall, Guerra-Carillo starts a doctoral program at the University of California, Berkeley, intending to explore what physically happens in the brain when people learn and how those changes affect academic performance.

Mangels’ other NSF-winning student, Jimena Santillan (Hunter, B.A. in psychology, 2012), starts a doctoral program at the University of Oregon this fall. An emigrant from Mexico where she attended an English-immersion school, Santillan intends to explore whether being bilingual helps people focus on what’s important while ignoring everything else that’s going on.

For her own research, Mangels examines “how we learn after we’ve made a mistake or experienced failure. I look at the mindsets and thought processes that interfere with learning. For example, I asked Jimena to look at rumination, the nonproductive chewing over of thoughts like ‘Why does this always happen to me?’, which take away mental energy without solving the problem.”

Her research has implications for teaching. Take what Mangels calls the “very American thing” of giving a medal to every kid in a race to boost the self-esteem of those who bring up the rear – or, by extension, giving lagging students some reward for their effort on a test. Does that help them learn? The preliminary evidence is yes, but only if the results are based on the effort they’ve put in.

“There are specific neurotransmitters that help us remember when we are rewarded – evolution biases organisms to remember rewarding things – but our recent findings suggest the reward makes an impact on learning only when you link it to the effort you’re putting into the task,” she says.

Funded by her Institute of Education Services award, Mangels sent Guerra-Carrillo into a New York City middle school to look at the impact of instructional interventions that could help students when they start to feel themselves struggle in a class or do poorly on a test.

“The amount of effort students put into learning after a failure depends a lot on whether they -- and their teachers -- think that the effort will pay off and they will see long-term improvement,” Mangels says.

Students who internalize this message of effort-based growth show up to a 10 percent difference in performance outcomes after failure. Her goal now is to work with researchers and educators to incorporate interventions promoting this message into everyday teaching practices.

There are implications for college classrooms as well. “We see students who get As in high school and suffer in college because they’re competing with other A students,” she says. “We’re looking at what mindsets can teachers encourage to get students focused less on performance and more on the learning process. We’re so focused on the test these days, not what students have to learn to do well.”

In her classroom, she tries to help students focus on learning and not the grade. Whether she is working one-on-one with a student in her lab or in front of 100 students in a class, it’s always an opportunity to mentor and help students reach their potential.

Mangels - Carillo



Bioinformatics and Computational Biology

Dr. Lei Xie

Associate Professor
Computer Science, Hunter College
Computer Science and Biology, CUNY Graduate Center
National Human Genome Research Institute
Young Investigator Award 2011

Vincent Xue

Macaulay Honors College at Hunter College
National Science Foundation
Graduate Research Fellow 2012

Viagra was originally developed to treat high blood pressure and heart disease. It didn’t work as planned, for researchers soon discovered a side effect that perhaps could be described as treatment for affairs of the heart.

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This unexpected turn of events was no tragedy for pharmaceutical giant Pfizer, which has made billions of dollars a year on that happy mistake. But wouldn’t it be better if researchers could rationally predict how drugs will work when they’re still in the test tube, rather than relying on trial and error after millions have been spent on development?

That’s one thing that Hunter College associate professor Lei Xie hopes to accomplish through the use of sophisticated computers and programs. In his Computational Systems Biology, Molecular Modeling and Bioinformatics Laboratory, he harnesses computers to study the structure, function, dynamics and evolution of molecular interactions on multiple scales, from the atomic level to biological networks. (Bioinformatics involves compiling and maintaining the database of biological information that has erupted since the dawn of genomics. Computational biology is the art and skill of analyzing and interpreting those data.)

“We’re trying to predict drug-target binding,” explains Xie (pronounced “sh-ye”). “The idea is that a drug will not bind to just one receptor, but to many, but most of them are unknown. Tens of thousands of proteins are related, so in a real situation, a drug could bind to many proteins – and we can predict which proteins they’ll bind to. Suppose we design drug A to bind to protein A. If we predict that the drug also binds to protein B -- and we know that protein B can cause another disease -- we can use this drug to treat this other disease. This will save a lot of money in drug development.”

This is the kind of exploration that Xie encourages the students he mentors to tackle. Among them is 2012 NSF Graduate Research Fellowship winner Vincent Xue (Macaulay Honors College at Hunter College, B.A. in computer science, minor in biology, 2012). He begins doctoral work at Massachusetts Institute of Technology this fall.

Working with his Hunter mentor, Xue (pronounced “sue”) developed a Web tool to analyze and visualize the effect of correlated amino acid mutations in proteins that enable cancer tumors to survive oxygen deprivation (hypoxia). Cancer can create oxygen-starved areas in solid tumors, and most solid tumors are more resilient to hypoxia than healthy organs. The body’s response to hypoxia thus can contribute to malignancy while offering a pathway to treatment: Turn off tumor cells’ ability to adapt to hypoxia, and you could kill the tumor.

Xie praised Xue’s work. “Hypoxia is quite complex, and we need new methods to understand it. Vincent focused on developing new methods to understand this genetic mutation.”

Researchers will need to continue developing such tools “because in biology we need to study how things work together at the same time, and that cannot be comprehended by humans,” he says. “That needs computers to mine this data.”

Xie is also conducting research in two other areas. He is looking into the mechanism through which drugs bind to protein. “We try to understand how strong a drug binds, as well as how long it binds to a protein,” he says. “This is a new paradigm that is related to drug efficacy. If a drug is to be more effective, it has to be stuck on its target protein longer.”

His third area of interest is understanding how multiple genetic mutations can work together to change phenotype, that is, the observed characteristics of an organism. The issue is intriguing because biological systems evolved with redundancy.

“Shutting down one pathway by removing a gene may not affect the final phenotype, so we need to understand how a change in function affects the whole biological system,” Xie says.

His research has been supported by awards from the National Institutes of Health, National Science Foundation, CUNY research initiative and pharmaceutical companies, including Optimer and Janssen. He also received a 2010 Genome Technology Young Investigator award and a 2012 Hunter President Award for Faculty Advancement.

Xie-Xue



Organic Chemistry

Dr. Barbara Zajc

Associate Professor
Organic Chemistry, City College
National Science Foundation
Research Award 2011-2013

Deborah Ayeni

City College
National Science Foundation
Graduate Research Fellow 2012

Undergraduate science students can earn diplomas without attempting original research, but as Barbara Zajc sees it, when those “who are motivated about science come into your lab and get involved in research, it opens the door to different career opportunities.”

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Zajc (pronounced “zyts”), an associate professor of chemistry at City College, enjoys her role as a mentor, particularly with standout students like 2012 NSF Graduate Research Fellowship winner Deborah Ayeni (City College, 2011). Now in a doctoral program in experimental pathology at the Yale School of Medicine, Ayeni says she intends to work with cancer-causing genes to seek “ways of interfering with cancer pathways, tumor regression and how cancers develop resistance to chemical agents.”

Ayeni, who was born in Nigeria, calls Zajc “a great mentor. I developed the skills I have from her. I e-mailed her about two minutes after I found out about the NSF fellowship.”

Zajc says that Ayeni “is an excellent student, very mature, very professional in her work habits and ethics, very motivated and focused. She kept coming into the lab on her own, whenever she had the time and on weekends, to finish her research work. I was very impressed with her analytic and critical thinking. She will do well in whatever career path she chooses.”

Zajc specializes in fluoroorganic chemistry. Speaking broadly, she develops new methods for chemically swapping fluorine atoms for hydrogen atoms in organic compounds. Fluorinated organic molecules have a wide range of applications, including in pharmaceuticals, in studying metabolism and in diagnostic tools like positron emission tomography (PET) scans. Inserting fluorine “can change the biological activity of a molecule. By comparing fluorinated molecules to their unfluorinated equivalents, you can learn a lot about cellular events,” she says. “A compound may be active, but you may not know why. If you change it a bit, the underlying difference can give you the answer.”

Her research has been supported by awards from the National Science Foundation, the National Institute of General Medical Sciences/Support of Competitive Research (SCORE) program, Bristol-Myers Squibb Undergraduate Research Awards (to support undergraduate research) and PSC-CUNY.

For her part, in addition to the NSF fellowship, Ayeni’s undergraduate research won her a CUNY-sponsored Jonas E. Salk Scholarship for graduate study. Working in Zajc’s lab, she explored the synthesis of fluorinated alkenes (used in pharmaceuticals and agrochemicals) through a process known as Julia-Kocienski olefination. She anticipates a career in industrial research, perhaps with a pharmaceutical or biotechnology company.

Zajc is mentoring two undergraduates, two master’s degree students and one doctoral student, Rakesh Kumar, who in September defended his dissertation on strategies in the modular synthesis of fluoroorganic compounds. Kumar is slated to conduct post-doctoral research at ETH, the Eidgenössische Technische Hochschule in Zurich, which is among the world’s top universities for engineering, science, technology, mathematics and management. A previous CCNY undergraduate student whom Zajc mentored, Maggie He, is also at ETH, where she is nearing completion of her Ph.D. degree in chemistry.

Undergraduates – most of them chemistry and biochemistry majors – usually start in Zajc’s lab as juniors after they have taken at least one organic chemistry course. The City College Academy of Professional Preparation refers some of the students. Some have taken her classes or read her research and are interested in her work.

“We have a very diverse student body. What I find very rewarding is that students can come from very underprivileged environments. Participating in research opens new avenues for them in terms of their careers and their lives,” she says. “When I hear from students who left my lab, and they say ‘I’m doing well’ or ‘I learned a lot,’ that’s what counts.”

Zajc-Ayeni